This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. At birth, an infant's gastrointestinal tract was thought to be sterile. In full term, healthy, breastfed infants, the intestinal colonization is dominated by health-promoting bacteria including Bifidobacterium and Lactobacillus (1-4). The pattern of enteric colonization is known to differ in infants and children with Cystic Fibrosis (CF) (5, 6). Within the first year of life, patients with CF become colonized with a typically select group of pathogenic bacteria. These organisms start the process of chronic infection, inflammation and progressive tissue damage in the airways. Thickened secretions also affect the GI system, including the pancreas and the intestines. Intestinal motility is slowed, causing constipation and in some cases obstruction (10, 11). Establishing a clear understanding of the developing microbiome in this high risk population prior to investigating potential targeted therapies with probiotics is imperative. Culture independent molecular techniques using 16S rRNA have improved the sensitivity of microbiome research, and massively parallel pyrosequencing (following DNA extraction and PCR amplification of rRNA variable regions) generates larger amounts of molecular sequence data allowing for more complete and precise investigation of the bacterial complexity of the intestinal microbiome community (18, 19). We are conducting a pilot study with 10 patients over the first year of life to investigate the developing intestinal and respiratory bacterial microbiota in infants with CF, using culture-independent 454 pyrosequencing (high throughput sequencing targeted at the bacterial 16s rRNA gene). We will link clinical information such as growth difficulties, respiratory infections to the microbial colonization patterns.